Link to this post | posted 07 Jan, 2019 17:52
masmith	Thank you.

Link to this post | posted 06 Jan, 2019 23:00

masmith

Hi, I am working on phage Pharaoh in the final stretch and keep questioning the DNA methylase. Two methylase genes are coming up in the A12 that are right next to each other, gp78 (ORF 47292 - 47942) and gp79 (ORF 47764-48306). The other two annotated A12 phages Steamy and DarthPhader both show significant overlap in these genes. I checked blast data, thinking maybe one really wasn't existing, but they are both coming with CP and blast results that are decent. I extended the first to its end, which gave 1:1 blast starts with multiple genes. This leads to a 179 overlap. I'm not sure what to do? I know the likelihood of this is not right, but what is going on? Any thoughts? Thanks. Mary Ann Edited 06 Jan, 2019 23:00 1.02Mb

Link to this post | posted 31 Jul, 2018 19:22

masmith

Hi, Gene 42 is the first gene after 2 tRNA genes in Typha. It was predicted as a reverse and has strong coding potential in the reverse. The other annotated Y phage has coding potential and call in the forward direction. The third Y phage does not have GeneMark files, so I can't check. Also, it the function to call is a question for me. Bipper (the other Y) has it listed as a ribonuclease toxin, which has support in HHPred. It's not an accepted function, but with little other support, I am not sure what to call it. I have the data I have attached. 1.58Mb

Link to this post | posted 31 Jul, 2018 19:01

masmith

Hi, So this will be the first of many posts. I've gone back and looked at my head-to-tail connector complex protein. I definitely have one with crystal support at Gene 15, but I am also getting crystal structure from PDB on the SPP1 phage with its portal (which I know it isn't as mine is upstream). My question/issue is that I'm confused on how to call this (if there is something to actually give it function) because on the PDB page it is also gives the listing with some match to the head-to-tail connector complex for the SPP1 phages in gene 16. It also happens on Typha on our Gene 18. I have the data attached for both. As this is the only other Cluster Y phage being annotated (out of the 3 currently existing), I am trying to make sure that all of the updates are included. Any help is appreciated. Thank you. Mary Ann 1.83Mb

Link to this post | posted 20 Mar, 2018 13:13

masmith

HI, We're confused and generally split about whether to leave gene 68 in Morty007 or delete it. We have evidence both ways and our twin Marley1013 has coding potential in the same region, but does not call the gene. The RBS data was Z score 1.967 and final score -4.800. I have attached a Word document with our evidence. Any thoughts out there to break our tie. Thank you in advance. Marywood PhageHunters 647Kb

Link to this post | posted 06 Apr, 2017 13:45
masmith	cdshaffer name: root password: phage Thank you - I've been sitting here for hours trying to get this work again. Very helpful.

Link to this post | posted 26 Jan, 2017 15:52
masmith	Hi again Welkin, I tried several more times this past week. We still are having the same problem. I'm going to try talking to our IT department. Do you have any other ideas on how to fix? Thanks. Mary Ann

Link to this post | posted 10 Jan, 2017 16:38

masmith

Hi, So we got our IT to load DNA Master to a lab of computers and to an instructor computer. I just went through to make sure everything was working correctly and found that all of the computers are giving me "FTP error." Didn't think much of it at first, but it won't let me change any of the preferences on the Local Settings, update settings or even save properly. The build number is 2346. I tried reinstalling with the copy of the software from my laptop and the same thing happened. (Note: our computers on campus keep timing out the Pitt site). I looked at site at Pitt and there was a slip-stream update. I downloaded it to another computer and disc to get the update, but don't know where to put it to even try to fix it. Any ideas. Thanks. Mary Ann